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Optics Express

Optics Express

  • Editor: C. Martijn de Sterke
  • Vol. 20, Iss. 14 — Jul. 2, 2012
  • pp: 16039–16049

PALMER: a method capable of parallel localization of multiple emitters for high-density localization microscopy

Yina Wang, Tingwei Quan, Shaoqun Zeng, and Zhen-Li Huang  »View Author Affiliations

Optics Express, Vol. 20, Issue 14, pp. 16039-16049 (2012)

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Developing methods for high-density localization of multiple emitters is a promising approach for enhancing the temporal resolution of localization microscopy while maintaining a desired spatial resolution, but the widespread use of this approach is thus far mainly obstructed by the slow image analysis speed. Here we present a high-density localization method based on the combination of Graphics Processing Unit (GPU) parallel computation, multiple-emitter fitting, and model recommendation via Bayesian Information Criterion (BIC). This method, called PALMER, exhibits satisfactory localization accuracy comparable with the previous reported SSM_BIC method, while executes more than two orders of magnitudes faster. Meanwhile, compared to the conventional localization microscopy which is based on sparse emitter localization, high-density localization microscopy based the PALMER method allows a speed gain of up to ~14-fold in obtaining a super-resolution image with the same Nyquist resolution.

© 2012 OSA

OCIS Codes
(100.6640) Image processing : Superresolution
(110.2960) Imaging systems : Image analysis
(180.2520) Microscopy : Fluorescence microscopy

ToC Category:
Image Processing

Original Manuscript: April 26, 2012
Revised Manuscript: June 13, 2012
Manuscript Accepted: June 21, 2012
Published: June 29, 2012

Virtual Issues
Vol. 7, Iss. 9 Virtual Journal for Biomedical Optics

Yina Wang, Tingwei Quan, Shaoqun Zeng, and Zhen-Li Huang, "PALMER: a method capable of parallel localization of multiple emitters for high-density localization microscopy," Opt. Express 20, 16039-16049 (2012)

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  1. K. R. Chi, “Super-resolution microscopy: breaking the limits,” Nat. Methods6(1), 15–18 (2009). [CrossRef]
  2. D. Toomre and J. Bewersdorf, “A new wave of cellular imaging,” Annu. Rev. Cell Dev. Biol.26(1), 285–314 (2010). [CrossRef] [PubMed]
  3. S. W. Hell, “Far-field optical nanoscopy,” Science316(5828), 1153–1158 (2007). [CrossRef] [PubMed]
  4. S. A. Jones, S. H. Shim, J. He, and X. W. Zhuang, “Fast, three-dimensional super-resolution imaging of live cells,” Nat. Methods8(6), 499–505 (2011). [CrossRef] [PubMed]
  5. E. Pastrana, “Fast 3D super-resolution fluorescence microscopy,” Nat. Methods8(1), 46 (2011). [CrossRef]
  6. H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods5(5), 417–423 (2008). [CrossRef] [PubMed]
  7. G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. W. Zhuang, “Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging,” Nat. Methods8(12), 1027–1036 (2011). [CrossRef] [PubMed]
  8. T. W. Quan, H. Y. Zhu, X. M. Liu, Y. F. Liu, J. P. Ding, S. Q. Zeng, and Z. L. Huang, “High-density localization of active molecules using Structured Sparse Model and Bayesian Information Criterion,” Opt. Express19(18), 16963–16974 (2011). [CrossRef] [PubMed]
  9. F. Huang, S. L. Schwartz, J. M. Byars, and K. A. Lidke, “Simultaneous multiple-emitter fitting for single molecule super-resolution imaging,” Biomed. Opt. Express2(5), 1377–1393 (2011). [CrossRef] [PubMed]
  10. S. J. Holden, S. Uphoff, and A. N. Kapanidis, “DAOSTORM: an algorithm for high- density super-resolution microscopy,” Nat. Methods8(4), 279–280 (2011). [CrossRef] [PubMed]
  11. S. Cox, E. Rosten, J. Monypenny, T. Jovanovic-Talisman, D. T. Burnette, J. Lippincott-Schwartz, G. E. Jones, and R. Heintzmann, “Bayesian localization microscopy reveals nanoscale podosome dynamics,” Nat. Methods9(2), 195–200 (2011). [CrossRef] [PubMed]
  12. L. Zhu, W. Zhang, D. Elnatan, and B. Huang, “Faster STORM using compressed sensing,” Nat Methods (2012), doi:. [CrossRef] [PubMed]
  13. S. Stallinga and B. Rieger, “Accuracy of the Gaussian Point Spread Function model in 2D localization microscopy,” Opt. Express18(24), 24461–24476 (2010). [CrossRef] [PubMed]
  14. B. Zhang, J. Zerubia, and J. C. Olivo-Marin, “Gaussian approximations of fluorescence microscope point-spread function models,” Appl. Opt.46(10), 1819–1829 (2007). [CrossRef] [PubMed]
  15. M. A. T. Figueiredo, R. D. Nowak, and S. J. Wright, “Gradient projection for sparse reconstruction: application to compressed sensing and other inverse problems,” IEEE J. Sel. Top. Signal Process.1(4), 586–597 (2007). [CrossRef]
  16. “GPU computing SDK, ” http://developer.nvidia.com/gpu-computing-sdk , accessed March 2012.
  17. Y. Cheng, “Mean shift, mode seeking, and clustering,” IEEE Trans. Pattern Anal. Mach. Intell.17(8), 790–799 (1995). [CrossRef]
  18. K. Nienhaus, G. U. Nienhaus, J. Wiedenmann, and H. Nar, “Structural basis for photo-induced protein cleavage and green-to-red conversion of fluorescent protein EosFP,” Proc. Natl. Acad. Sci. U.S.A.102(26), 9156–9159 (2005). [CrossRef] [PubMed]
  19. Z. Gao, Y. Lai, and Z. Hu, “A generalized gradient projection method for optimization problems with equality and inequality constraints about arbitrary initial point,” Acta Appl. Math.12(1), 40–49 (1996). [CrossRef]
  20. T. W. Quan, P. C. Li, F. Long, S. Q. Zeng, Q. M. Luo, P. N. Hedde, G. U. Nienhaus, and Z. L. Huang, “Ultra-fast, high-precision image analysis for localization-based super resolution microscopy,” Opt. Express18(11), 11867–11876 (2010). [CrossRef] [PubMed]

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